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-rw-r--r--sci-libs/arrayfire/arrayfire-3.7.2.ebuild2
-rw-r--r--sci-libs/arrayfire/arrayfire-3.7.3.ebuild2
-rw-r--r--sci-libs/arrayfire/arrayfire-3.8.0.ebuild2
-rw-r--r--sci-libs/asl/asl-0.1.7.ebuild2
-rw-r--r--sci-libs/asl/asl-9999.ebuild2
-rw-r--r--sci-libs/daal4py/daal4py-2023.0.2.ebuild2
-rw-r--r--sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch69
-rw-r--r--sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch72
-rw-r--r--sci-libs/gdcm/gdcm-3.0.14.ebuild2
-rw-r--r--sci-libs/gvar/Manifest1
-rw-r--r--sci-libs/gvar/gvar-13.0.2.ebuild22
-rw-r--r--sci-libs/gvar/metadata.xml19
-rw-r--r--sci-libs/handyg/files/handyg-0.1.5-ld.patch22
-rw-r--r--sci-libs/itk/itk-5.2.1-r2.ebuild2
-rw-r--r--sci-libs/itk/itk-5.3.0-r1.ebuild2
-rw-r--r--sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch11
-rw-r--r--sci-libs/mpfun90/Manifest1
-rw-r--r--sci-libs/mpfun90/metadata.xml18
-rw-r--r--sci-libs/mpfun90/mpfun90-2023.02.26.ebuild29
-rw-r--r--sci-libs/nexus/nexus-4.4.3_p20200126.ebuild2
-rw-r--r--sci-libs/nibabel/Manifest2
-rw-r--r--sci-libs/nibabel/nibabel-5.1.0.ebuild (renamed from sci-libs/nibabel/nibabel-4.0.0.ebuild)10
-rw-r--r--sci-libs/nipy/Manifest2
-rw-r--r--sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild52
-rw-r--r--sci-libs/nipy/nipy-0.6.0.ebuild37
-rw-r--r--sci-libs/nipype/Manifest2
-rw-r--r--sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch50
-rw-r--r--sci-libs/nipype/nipype-1.8.4-r1.ebuild1
-rw-r--r--sci-libs/nipype/nipype-1.8.4-r2.ebuild (renamed from sci-libs/nipype/nipype-1.5.0.ebuild)22
-rw-r--r--sci-libs/nipype/nipype-1.8.6.ebuild97
-rw-r--r--sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild4
-rw-r--r--sci-libs/torchvision/Manifest1
-rw-r--r--sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch36
-rw-r--r--sci-libs/torchvision/torchvision-0.17.1.ebuild45
-rw-r--r--sci-libs/vegas/Manifest1
-rw-r--r--sci-libs/vegas/metadata.xml19
-rw-r--r--sci-libs/vegas/vegas-6.0.1.ebuild24
-rw-r--r--sci-libs/wannier90/files/wannier90-1.1-0001.patch16
-rw-r--r--sci-libs/wannier90/files/wannier90-1.1-0002.patch105
-rw-r--r--sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch12
40 files changed, 430 insertions, 392 deletions
diff --git a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.7.2.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.7.3.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
index eb8917457..5d2f3c7a4 100644
--- a/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
+++ b/sci-libs/arrayfire/arrayfire-3.8.0.ebuild
@@ -44,7 +44,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
virtual/pkgconfig
"
diff --git a/sci-libs/asl/asl-0.1.7.ebuild b/sci-libs/asl/asl-0.1.7.ebuild
index 50eaeea5d..cbfbde5c6 100644
--- a/sci-libs/asl/asl-0.1.7.ebuild
+++ b/sci-libs/asl/asl-0.1.7.ebuild
@@ -26,7 +26,7 @@ RDEPEND="
DEPEND="${RDEPEND}
matlab? ( >=sci-libs/matio-1.5.2 )
"
-BDEPEND="doc? ( app-doc/doxygen[dot] )"
+BDEPEND="doc? ( app-text/doxygen[dot] )"
S="${WORKDIR}/${MY_PN}-${PV}"
diff --git a/sci-libs/asl/asl-9999.ebuild b/sci-libs/asl/asl-9999.ebuild
index 82b464f7f..905c8813a 100644
--- a/sci-libs/asl/asl-9999.ebuild
+++ b/sci-libs/asl/asl-9999.ebuild
@@ -24,7 +24,7 @@ RDEPEND="
DEPEND="${RDEPEND}
matlab? ( >=sci-libs/matio-1.5.2 )
"
-BDEPEND="doc? ( app-doc/doxygen[dot] )"
+BDEPEND="doc? ( app-text/doxygen[dot] )"
src_prepare() {
cmake_src_prepare
diff --git a/sci-libs/daal4py/daal4py-2023.0.2.ebuild b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
index 09fc690fd..f23e1c738 100644
--- a/sci-libs/daal4py/daal4py-2023.0.2.ebuild
+++ b/sci-libs/daal4py/daal4py-2023.0.2.ebuild
@@ -19,7 +19,7 @@ KEYWORDS="~amd64"
BDEPEND="
dev-python/cython[${PYTHON_USEDEP}]
dev-python/pybind11[${PYTHON_USEDEP}]
- dev-util/cmake
+ dev-build/cmake
sys-devel/DPC++
test? (
sci-libs/scikit-learn[${PYTHON_USEDEP}]
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
deleted file mode 100644
index 5d3754d56..000000000
--- a/sci-libs/daal4py/files/daal4py-2021.7.1-dont-use-entire-include.patch
+++ /dev/null
@@ -1,69 +0,0 @@
-diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
-index 203c870..7fdac1e 100755
---- a/generator/gen_daal4py.py
-+++ b/generator/gen_daal4py.py
-@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
- enum_maps, enum_params, wrap_algo, result_to_compute)
- from .wrapper_gen import wrapper_gen
- from .format import mk_var
--from shutil import copytree, rmtree
-+from shutil import copytree, copyfile, rmtree
- from subprocess import call
-
- try:
-@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
- head_path = jp("build", "include")
- algo_path = jp(head_path, "algorithms")
- rmtree(head_path, ignore_errors=True)
-- copytree(orig_path, head_path)
-+ copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
-+ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
-+ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
-+ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
-+ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
-+ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
-+ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
- for (dirpath, dirnames, filenames) in os.walk(algo_path):
- for filename in filenames:
- call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
-diff --git a/scripts/build_backend.py b/scripts/build_backend.py
-index a252a1d..c36a312 100755
---- a/scripts/build_backend.py
-+++ b/scripts/build_backend.py
-@@ -116,10 +116,8 @@ def custom_build_cmake_clib(iface, cxx=None):
- python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
- numpy_include = np.get_include()
-
-- if iface == 'dpc':
-- cxx = 'dpcpp'
-- elif cxx is None:
-- raise RuntimeError('CXX compiler shall be specified')
-+ if cxx is None:
-+ cxx=os.environ.get('CXX')
-
- cmake_args = [
- "cmake",
-diff --git a/setup.py b/setup.py
-index 864ab5d..7eaa52f 100755
---- a/setup.py
-+++ b/setup.py
-@@ -47,7 +47,7 @@ if dal_root is None:
-
- if 'linux' in sys.platform:
- IS_LIN = True
-- lib_dir = jp(dal_root, 'lib', 'intel64')
-+ lib_dir = jp(dal_root, 'lib64')
- elif sys.platform == 'darwin':
- IS_MAC = True
- lib_dir = jp(dal_root, 'lib')
-@@ -306,8 +306,8 @@ def build_oneapi_backend():
- eca, ela, includes = get_build_options()
-
- return build_backend.build_cpp(
-- cc='dpcpp',
-- cxx='dpcpp',
-+ cc=os.environ.get('CC'),
-+ cxx=os.environ.get('CXX'),
- sources=['src/oneapi/oneapi_backend.cpp'],
- targetname='oneapi_backend',
- targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch b/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch
deleted file mode 100644
index 9ccf0f156..000000000
--- a/sci-libs/daal4py/files/daal4py-2021.7.1_p20221209-dont-use-entire-include.patch
+++ /dev/null
@@ -1,72 +0,0 @@
-diff --git a/generator/gen_daal4py.py b/generator/gen_daal4py.py
-index 203c870..7fdac1e 100755
---- a/generator/gen_daal4py.py
-+++ b/generator/gen_daal4py.py
-@@ -34,7 +34,7 @@ from .wrappers import (required, ignore, defaults, has_dist, ifaces,
- enum_maps, enum_params, wrap_algo, result_to_compute)
- from .wrapper_gen import wrapper_gen
- from .format import mk_var
--from shutil import copytree, rmtree
-+from shutil import copytree, copyfile, rmtree
- from subprocess import call
-
- try:
-@@ -1045,7 +1045,13 @@ def gen_daal4py(daalroot, outdir, version, warn_all=False,
- head_path = jp("build", "include")
- algo_path = jp(head_path, "algorithms")
- rmtree(head_path, ignore_errors=True)
-- copytree(orig_path, head_path)
-+ copytree(jp(orig_path, 'services'), jp(head_path, 'services'))
-+ copytree(jp(orig_path, 'oneapi', 'dal'), jp(head_path, 'oneapi', 'dal'))
-+ copytree(jp(orig_path, 'data_management'), jp(head_path, 'data_management'))
-+ copytree(jp(orig_path, 'algorithms'), jp(head_path, 'algorithms'))
-+ copyfile(jp(orig_path, 'daal.h'), jp(head_path, 'daal.h'))
-+ copyfile(jp(orig_path, 'daal_sycl.h'), jp(head_path, 'daal_sycl.h'))
-+ copyfile(jp(orig_path, 'oneapi', 'dal.hpp'), jp(head_path, 'oneapi', 'dal.hpp'))
- for (dirpath, dirnames, filenames) in os.walk(algo_path):
- for filename in filenames:
- call([shutil.which("clang-format"), "-i", jp(dirpath, filename)])
-diff --git a/scripts/build_backend.py b/scripts/build_backend.py
-index bb38056..7216983 100755
---- a/scripts/build_backend.py
-+++ b/scripts/build_backend.py
-@@ -115,13 +115,8 @@ def custom_build_cmake_clib(iface, cxx=None):
- python_library_dir = win_python_path_lib if IS_WIN else get_config_var('LIBDIR')
- numpy_include = np.get_include()
-
-- if iface == 'dpc':
-- if IS_WIN:
-- cxx = 'icx'
-- else:
-- cxx = 'icpx'
-- elif cxx is None:
-- raise RuntimeError('CXX compiler shall be specified')
-+ if cxx is None:
-+ cxx=os.environ.get('CXX')
-
- cmake_args = [
- "cmake",
-diff --git a/setup.py b/setup.py
-index 00b4f43..76857a2 100755
---- a/setup.py
-+++ b/setup.py
-@@ -47,7 +47,7 @@ if dal_root is None:
-
- if 'linux' in sys.platform:
- IS_LIN = True
-- lib_dir = jp(dal_root, 'lib', 'intel64')
-+ lib_dir = jp(dal_root, 'lib64')
- elif sys.platform == 'darwin':
- IS_MAC = True
- lib_dir = jp(dal_root, 'lib')
-@@ -313,8 +313,8 @@ def build_oneapi_backend():
- eca += ['-fsycl']
-
- return build_backend.build_cpp(
-- cc=cc,
-- cxx=cxx,
-+ cc=os.environ.get('CC'),
-+ cxx=os.environ.get('CXX'),
- sources=['src/oneapi/oneapi_backend.cpp'],
- targetname='oneapi_backend',
- targetprefix='' if IS_WIN else 'lib',
diff --git a/sci-libs/gdcm/gdcm-3.0.14.ebuild b/sci-libs/gdcm/gdcm-3.0.14.ebuild
index 10f1d3b50..c1000fea9 100644
--- a/sci-libs/gdcm/gdcm-3.0.14.ebuild
+++ b/sci-libs/gdcm/gdcm-3.0.14.ebuild
@@ -40,7 +40,7 @@ RDEPEND="${DEPEND}"
BDEPEND="
dev-libs/libxslt
app-text/docbook-xsl-ns-stylesheets
- doc? ( app-doc/doxygen[dot] )
+ doc? ( app-text/doxygen[dot] )
python? (
${PYTHON_DEPS}
>=dev-lang/swig-3.0.7
diff --git a/sci-libs/gvar/Manifest b/sci-libs/gvar/Manifest
new file mode 100644
index 000000000..16bdf1de2
--- /dev/null
+++ b/sci-libs/gvar/Manifest
@@ -0,0 +1 @@
+DIST gvar-13.0.2.tar.gz 1001282 BLAKE2B 5c4032406e3d514351bac6f21b5353c8db4e2081efd26b758cce126cce4a3df350ac8086e89895c73ffc27367773a43354138e8598490cbe8f7bacdde216f0bd SHA512 541cb5cc44909cf44e9f808a08a959aa5e3e91c49356fb8865879a9dbb5fe6f3c4b46d88bc4f9346d9b83163c938dfd697e73b7b9a00815ed6dc383630795cb4
diff --git a/sci-libs/gvar/gvar-13.0.2.ebuild b/sci-libs/gvar/gvar-13.0.2.ebuild
new file mode 100644
index 000000000..b9d9121e4
--- /dev/null
+++ b/sci-libs/gvar/gvar-13.0.2.ebuild
@@ -0,0 +1,22 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Gaussian random variables."
+HOMEPAGE="https://github.com/gplepage/gvar"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+ >=dev-python/cython-0.17[${PYTHON_USEDEP}]
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+"
+BDEPEND="${RDEPEND}"
+
+distutils_enable_tests unittest
diff --git a/sci-libs/gvar/metadata.xml b/sci-libs/gvar/metadata.xml
new file mode 100644
index 000000000..31346f0dd
--- /dev/null
+++ b/sci-libs/gvar/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ This package facilitates the creation and manipulation of arbitrarily complicated (correlated) multi-dimensional Gaussian random variables. The random variables are represented by a new data type (gvar.GVar) that can be used in arithmetic expressions and pure Python functions. Such expressions/functions create new Gaussian random variables while automatically tracking statistical correlations between the new and old variables. This data type is useful for simple error propagation, but also is heavily used by the Bayesian least-squares fitting module lsqfit.py to define priors and specify fit results, while accounting for correlations between all variables.
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">gvar</remote-id>
+ <remote-id type="github">gplepage/gvar</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/handyg/files/handyg-0.1.5-ld.patch b/sci-libs/handyg/files/handyg-0.1.5-ld.patch
deleted file mode 100644
index f3f06cd91..000000000
--- a/sci-libs/handyg/files/handyg-0.1.5-ld.patch
+++ /dev/null
@@ -1,22 +0,0 @@
---- a/configure 2022-09-19 01:59:40.382091704 +0200
-+++ b/configure 2022-09-19 02:00:00.734380534 +0200
-@@ -358,7 +358,7 @@
- FLDFLAGS+=" $1" ;;
- -Bstatic | -Bdynamic | *.ld)
- echo "Found linker flag $1" 1>&2
-- FLDFLAGS+=" -Wl,$1" ;;
-+ FLDFLAGS+=" $1" ;;
- /*)
- echo "Found linker flag $1" 1>&2
- FLDFLAGS+=" -L$1" ;;
---- a/configure 2022-09-19 02:02:18.064324729 +0200
-+++ b/configure 2022-09-19 02:02:22.935393539 +0200
-@@ -364,7 +364,7 @@
- FLDFLAGS+=" -L$1" ;;
- -rpath*)
- echo "Found linker flag $1" 1>&2
-- FLDFLAGS+=" -Wl,$1,$2"
-+ FLDFLAGS+=" $1,$2"
- shift ;;
- -dynamic-linker)
- shift ;;
diff --git a/sci-libs/itk/itk-5.2.1-r2.ebuild b/sci-libs/itk/itk-5.2.1-r2.ebuild
index 1aa0dc43a..0b1f25860 100644
--- a/sci-libs/itk/itk-5.2.1-r2.ebuild
+++ b/sci-libs/itk/itk-5.2.1-r2.ebuild
@@ -71,7 +71,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
"
BDEPEND="
test? (
diff --git a/sci-libs/itk/itk-5.3.0-r1.ebuild b/sci-libs/itk/itk-5.3.0-r1.ebuild
index 29a3da5d0..b2c3af801 100644
--- a/sci-libs/itk/itk-5.3.0-r1.ebuild
+++ b/sci-libs/itk/itk-5.3.0-r1.ebuild
@@ -79,7 +79,7 @@ DEPEND="${RDEPEND}
>=dev-lang/swig-2.0:0
dev-libs/castxml
)
- doc? ( app-doc/doxygen )
+ doc? ( app-text/doxygen )
"
BDEPEND="
test? (
diff --git a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch b/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
deleted file mode 100644
index 0f64b325f..000000000
--- a/sci-libs/lib2bit/files/lib2bit-0.2.1_respect_DESTDIR.patch
+++ /dev/null
@@ -1,11 +0,0 @@
---- lib2bit-0.2.1/Makefile.ori 2017-03-31 22:09:48.387098439 +0200
-+++ lib2bit-0.2.1/Makefile 2017-03-31 22:10:29.889020564 +0200
-@@ -8,7 +8,7 @@
- LDLIBS =
- INCLUDES =
-
--prefix = /usr/local
-+prefix = $(DESTDIR)/usr/local
- includedir = $(prefix)/include
- libdir = $(exec_prefix)/lib
-
diff --git a/sci-libs/mpfun90/Manifest b/sci-libs/mpfun90/Manifest
new file mode 100644
index 000000000..56d64f14c
--- /dev/null
+++ b/sci-libs/mpfun90/Manifest
@@ -0,0 +1 @@
+DIST 2023-02-26.tar.gz 66883 BLAKE2B 3b93099977b614e0d9a16df76f7f3c1eda9b76905664db3f0dc0ad0bd00b503105649aeb4c960d7293e7d536e3a902dbe8cb62f89be3bce655e9bae963097f35 SHA512 7280ecba6cb95f15cea91ea95f5cf21b69f76a490a3c92bef40cf8a1dfadd651cb93480bddddd684d0f18144db65cdb1590964df11d37a9f35eaeeb94f369d63
diff --git a/sci-libs/mpfun90/metadata.xml b/sci-libs/mpfun90/metadata.xml
new file mode 100644
index 000000000..e3eb0d9c1
--- /dev/null
+++ b/sci-libs/mpfun90/metadata.xml
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <maintainer type="project">
+ <email>sci-physics@gentoo.org</email>
+ <name>Gentoo Physics Project</name>
+ </maintainer>
+ <longdescription lang="en">
+ This package permits one to perform floating-point computations (real and complex) to arbitrarily high numeric precision
+ </longdescription>
+ <upstream>
+ <remote-id type="github">APN-Pucky/mpfun90</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
new file mode 100644
index 000000000..4f885fa2c
--- /dev/null
+++ b/sci-libs/mpfun90/mpfun90-2023.02.26.ebuild
@@ -0,0 +1,29 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+inherit toolchain-funcs fortran-2
+
+DESCRIPTION="High-Precision Software"
+HOMEPAGE="
+ https://www.davidhbailey.com/dhbsoftware/
+ https://github.com/APN-Pucky/mpfun90
+"
+MY_PV=$(ver_rs 1- '-')
+SRC_URI="https://github.com/APN-Pucky/mpfun90/archive/refs/tags/${MY_PV}.tar.gz"
+S="${WORKDIR}/mpfun90-${MY_PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+
+src_compile() {
+ emake -j1 dynamic
+}
+
+src_install() {
+ doheader *.mod
+ dolib.so libmpfun90.so
+ dolib.a libmpfun90.a
+}
diff --git a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
index b19a65fbe..58d8264cf 100644
--- a/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
+++ b/sci-libs/nexus/nexus-4.4.3_p20200126.ebuild
@@ -29,7 +29,7 @@ RDEPEND="
"
DEPEND="${RDEPEND}"
BDEPEND="
- app-doc/doxygen[dot]
+ app-text/doxygen[dot]
"
pkg_setup() {
diff --git a/sci-libs/nibabel/Manifest b/sci-libs/nibabel/Manifest
index 4bc4a8fd6..d50b1b3b7 100644
--- a/sci-libs/nibabel/Manifest
+++ b/sci-libs/nibabel/Manifest
@@ -1,2 +1,2 @@
-DIST nibabel-4.0.0.tar.gz 4505565 BLAKE2B 5efee05adbb0ff9204218060f75acdf6b5b77a1a7cc9b884d122f4a95805f6110a0d9433946d4a53d3aa615932012effe35b4ffa9773fb992da8ff273bf3cfd7 SHA512 1b34901e69ff7aaabfb94e49199de761eb7e397a0a7360c2077935d250368cd061cf1fa9c6ef561fa7707e4853c421b039818bfa4b32fc4792555f3d6235eeb7
DIST nibabel-5.0.0.tar.gz 4480342 BLAKE2B ef5c8fcd27fda60ae85fb657b360453a3b6ae58ea2b8e4eb55bfeb4bdecf6aa94cf1594d0b90a3187f6f3bad32fa9c721bba0827ec0966f799e5b59720778956 SHA512 5f27c03518c47856ecb33b878e9969ea33c7ebb717e6f4f9d89d9fdf415459e47675353051cdb824efea4e6a819759e0bf61cf49caa7212411c63423a77ed0d4
+DIST nibabel-5.1.0.tar.gz 4522882 BLAKE2B 62ffd86e14f66ab57bcfa127e9d0da0b46a04224739b61493080848305295f25136b51bc6fae69c0ec653b4185a28a1b5c323573588abc02f6ebb7372808b8fe SHA512 a07b4c2742ac3af8c0a87a0fa0562ed55c1377fb2067a7813fa2482cab4fc407f013b13b541dd863fa9620c644058296040487aeaba0b26818ff783b2dc2474e
diff --git a/sci-libs/nibabel/nibabel-4.0.0.ebuild b/sci-libs/nibabel/nibabel-5.1.0.ebuild
index 4a24fb940..0fec805b1 100644
--- a/sci-libs/nibabel/nibabel-4.0.0.ebuild
+++ b/sci-libs/nibabel/nibabel-5.1.0.ebuild
@@ -4,7 +4,7 @@
EAPI=8
PYTHON_COMPAT=( python3_{10..11} )
-DISTUTILS_USE_SETUPTOOLS=rdepend
+DISTUTILS_USE_PEP517=hatchling
inherit distutils-r1
@@ -27,11 +27,9 @@ RDEPEND="
)
"
-EPYTEST_DESELECT=(
- # Rported upstream:
- # https://github.com/nipy/nibabel/issues/1191
- nibabel/tests/test_volumeutils.py::test_a2f_nan2zero_range
-)
+BDEPEND="test? (
+ dev-python/pytest-httpserver[${PYTHON_USEDEP}]
+)"
distutils_enable_sphinx doc/source dev-python/texext dev-python/numpydoc dev-python/matplotlib
distutils_enable_tests pytest
diff --git a/sci-libs/nipy/Manifest b/sci-libs/nipy/Manifest
index 362628814..9444a9dd3 100644
--- a/sci-libs/nipy/Manifest
+++ b/sci-libs/nipy/Manifest
@@ -1 +1 @@
-DIST nipy-0.5.1_pre20230103.gh.tar.gz 2462662 BLAKE2B 0e6aa24875e514bf16280e20bb3059027ad30c3d510db62b0ed80b33724aacb0a20260f7cf9d87858a9da5d07fab58535cee1306fe2b7be7a72364156197aeab SHA512 7ed89b5e637159c90893a02dd9481a662f7e589fc6fe76c3e7919231144a56668815edc0f57a77728a9c95c7640e474563e922609c56cd0ad0fcfbd3c5bdb6bd
+DIST nipy-0.6.0.gh.tar.gz 1650342 BLAKE2B 5f375e23fb2d895cfb4320b8ec92cefcf902f3768b6b8dc2ba26b4db30168eb4a29d38be1241e2ae5ae9d87013beb64427c8aca1ac2adaa92d083c700dc0453a SHA512 a59485ccd677c443b9d1e2358c3b3d523ddfa9f390c180661e9afaf3b69943e1b1670c44410954e1bba11c88b9ca20e9e586392804b5c99e9f58b5b68df4641f
diff --git a/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild b/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild
deleted file mode 100644
index 25bdee0b8..000000000
--- a/sci-libs/nipy/nipy-0.5.1_pre20230103.ebuild
+++ /dev/null
@@ -1,52 +0,0 @@
-# Copyright 1999-2023 Gentoo Authors
-# Distributed under the terms of the GNU General Public License v2
-
-EAPI=8
-
-PYTHON_COMPAT=( python3_{10..11} )
-
-inherit distutils-r1
-
-MY_HASH="35a5f5205ba2aa54f1f0524564a6f1f8dafb237f"
-
-DESCRIPTION="Neuroimaging tools for Python"
-HOMEPAGE="https://nipy.org/"
-SRC_URI="https://github.com/${PN}/${PN}/archive/${MY_HASH}.tar.gz -> ${P}.gh.tar.gz"
-
-LICENSE="BSD"
-SLOT="0"
-KEYWORDS="~amd64 ~x86"
-IUSE=""
-
-RDEPEND="
- dev-python/scipy[${PYTHON_USEDEP}]
- dev-python/sympy[${PYTHON_USEDEP}]
- sci-libs/nibabel[${PYTHON_USEDEP}]
- dev-python/numpy[${PYTHON_USEDEP}]
- "
-DEPEND=""
-
-S="${WORKDIR}/${PN}-${MY_HASH}"
-
-python_prepare_all() {
- distutils-r1_python_prepare_all
- # bug #397605
- [[ ${CHOST} == *-darwin* ]] \
- && append-ldflags -bundle "-undefined dynamic_lookup" \
- || append-ldflags -shared
-
- # nipy uses the horrible numpy.distutils automagic
-}
-
-#python_test() {
-# distutils-r1_install_for_testing
-# cp nipy/testing/*.nii.gz "${BUILD_DIR}/lib/nipy/testing/"
-# cp nipy/modalities/fmri/tests/*.{mat,npz,txt} "${BUILD_DIR}/lib/nipy/modalities/fmri/tests/"
-# cp nipy/algorithms/statistics/models/tests/test_data.bin "${BUILD_DIR}/lib/nipy/algorithms/statistics/models/tests"
-# cp nipy/labs/spatial_models/tests/some_blobs.nii "${BUILD_DIR}/lib/nipy/labs/spatial_models/tests/some_blobs.nii"
-# mkdir "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-# cp nipy/algorithms/diagnostics/tests/data/tsdiff_results.mat "${BUILD_DIR}/lib/nipy/algorithms/diagnostics/tests/data/"
-# cd "${BUILD_DIR}" || die
-# echo "backend : agg" > matplotlibrc
-# nosetests || die
-#}
diff --git a/sci-libs/nipy/nipy-0.6.0.ebuild b/sci-libs/nipy/nipy-0.6.0.ebuild
new file mode 100644
index 000000000..8f8ea83e8
--- /dev/null
+++ b/sci-libs/nipy/nipy-0.6.0.ebuild
@@ -0,0 +1,37 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=meson-python
+PYTHON_COMPAT=( python3_{10..11} )
+DISTUTILS_EXT=1
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging tools for Python"
+HOMEPAGE="https://nipy.org/"
+SRC_URI="https://github.com/nipy/nipy/archive/refs/tags/${PV}.tar.gz -> ${P}.gh.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE=""
+# Test data unavailable:
+# https://github.com/nipy/nipy/issues/561#event-11866547632
+RESTRICT="test"
+
+RDEPEND="
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/sympy[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ dev-python/numpy[${PYTHON_USEDEP}]
+ "
+DEPEND=""
+
+distutils_enable_tests pytest
+
+python_test() {
+ rm -rf nipy || die
+ epytest
+}
diff --git a/sci-libs/nipype/Manifest b/sci-libs/nipype/Manifest
index a2ffd1d7a..6c9059e1c 100644
--- a/sci-libs/nipype/Manifest
+++ b/sci-libs/nipype/Manifest
@@ -1,2 +1,2 @@
-DIST nipype-1.5.0.tar.gz 2735317 BLAKE2B d618714b15defde52325bac32a80449846b448d1c141a21f9d950976c8c89624d714dbab10b4cd99fe20d4eb99ceb4095ebc6ddc567f57b3803e2c16ffda155a SHA512 eb11096a090855278c3e76ffe9643ab4de046a017511ba51f59448fd8cf9d67a4f6c552acbbbdd38065cfb456c24fd21299cf698fa05c5be507524622f28ac85
DIST nipype-1.8.4.tar.gz 2914433 BLAKE2B c25b82c22641f6df2b57c8a07fd318034bb4fe4eaa1037baebc1ffc03d3e1add347d9f0c94139144fc17043a5c97926c88b40755f19794cc71366d76ba339698 SHA512 8949226accd7c158b6a3ec92389a11760a9b306098ccb8ef50844efbddb4e6a9108bb6a32ec7b0402c4ea56881a3548b052fe7f5e757d2771aea5b2eebc9377b
+DIST nipype-1.8.6.tar.gz 2921102 BLAKE2B 79a2131b8265f1b0a3a8d2fa6ff56cbbc2d393c79099178cf036d82357a971a72f024b132d7b4d7d4af85165f562192b6cc5cfc9e797105bdc009734e8a89033 SHA512 23140beb02f4c3807d9d0291bde41ce8c1b06e48dc94001b007f193caaa89428387d1528fa20ae328d2c4a781024c9acf07f7be9ce507ecb2f1daf338c092eec
diff --git a/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
new file mode 100644
index 000000000..b5c223422
--- /dev/null
+++ b/sci-libs/nipype/files/nipype-1.8.4-no_etelemetry.patch
@@ -0,0 +1,50 @@
+diff --git a/nipype/__init__.py b/nipype/__init__.py
+index 06084e823..2e42dcbce 100644
+--- a/nipype/__init__.py
++++ b/nipype/__init__.py
+@@ -73,23 +73,6 @@ from .interfaces import (
+ )
+
+
+-def check_latest_version(raise_exception=False):
+- """
+- Check for the latest version of the library.
+-
+- Parameters
+- ----------
+- raise_exception: bool
+- Raise a RuntimeError if a bad version is being used
+- """
+- import etelemetry
+-
+- logger = logging.getLogger("nipype.utils")
+- return etelemetry.check_available_version(
+- "nipy/nipype", __version__, logger, raise_exception
+- )
+-
+-
+ # Run telemetry on import for interactive sessions, such as IPython, Jupyter notebooks, Python REPL
+ if config.getboolean("execution", "check_version"):
+ import __main__
+@@ -98,4 +81,4 @@ if config.getboolean("execution", "check_version"):
+ from .interfaces.base import BaseInterface
+
+ if BaseInterface._etelemetry_version_data is None:
+- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++ BaseInterface._etelemetry_version_data = "n/a"
+diff --git a/nipype/interfaces/base/core.py b/nipype/interfaces/base/core.py
+index c8099be63..f7770dbfc 100644
+--- a/nipype/interfaces/base/core.py
++++ b/nipype/interfaces/base/core.py
+@@ -183,10 +183,9 @@ class BaseInterface(Interface):
+ config.getboolean("execution", "check_version")
+ and "NIPYPE_NO_ET" not in os.environ
+ ):
+- from ... import check_latest_version
+
+ if BaseInterface._etelemetry_version_data is None:
+- BaseInterface._etelemetry_version_data = check_latest_version() or "n/a"
++ BaseInterface._etelemetry_version_data = "n/a"
+
+ if not self.input_spec:
+ raise Exception("No input_spec in class: %s" % self.__class__.__name__)
diff --git a/sci-libs/nipype/nipype-1.8.4-r1.ebuild b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
index 8214ccff4..7c2e801ff 100644
--- a/sci-libs/nipype/nipype-1.8.4-r1.ebuild
+++ b/sci-libs/nipype/nipype-1.8.4-r1.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
diff --git a/sci-libs/nipype/nipype-1.5.0.ebuild b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
index 750c3ba05..4c3da70b3 100644
--- a/sci-libs/nipype/nipype-1.5.0.ebuild
+++ b/sci-libs/nipype/nipype-1.8.4-r2.ebuild
@@ -3,6 +3,7 @@
EAPI=8
+DISTUTILS_USE_PEP517=setuptools
PYTHON_COMPAT=( python3_{10..11} )
PYTHON_REQ_USE="threads(+),sqlite"
@@ -28,30 +29,29 @@ DEPEND="
${RDEPEND}
)
"
-# Dependency disabled as upstream test configuration which requires it fails
-#dev-python/pytest-xdist[${PYTHON_USEDEP}]
RDEPEND="
- >=dev-python/click-6.6[${PYTHON_USEDEP}]
+ dev-python/click[${PYTHON_USEDEP}]
dev-python/filelock[${PYTHON_USEDEP}]
+ dev-python/looseversion[${PYTHON_USEDEP}]
dev-python/networkx[${PYTHON_USEDEP}]
dev-python/packaging[${PYTHON_USEDEP}]
dev-python/pydot[${PYTHON_USEDEP}]
- dev-python/pydotplus[${PYTHON_USEDEP}]
dev-python/python-dateutil[${PYTHON_USEDEP}]
- >=dev-python/rdflib-5.0.0[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
dev-python/scipy[${PYTHON_USEDEP}]
dev-python/simplejson[${PYTHON_USEDEP}]
- dev-python/traits[${PYTHON_USEDEP}]
+ <dev-python/traits-6.4.0[${PYTHON_USEDEP}]
"
PATCHES=(
- "${FILESDIR}/${P}"-version_check.patch
- "${FILESDIR}/${P}"-collections.patch
+ "${FILESDIR}/${PN}-1.8.4-dependency_compatibility.patch"
+ "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
)
src_prepare() {
# Remove etelemetry
+ # Doing this separately since the file is affected by another patch.
sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
# Mark failing tests
@@ -69,12 +69,10 @@ python_install_all() {
doenvd "${FILESDIR}/98nipype"
}
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
EPYTEST_DESELECT=(
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_compcor_variance_threshold_and_metadata
- nipype/algorithms/tests/test_CompCor.py::TestCompCor::test_tcompcor
nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
- nipype/utils/tests/test_cmd.py::TestNipypeCMD::test_main_returns_0_on_help
)
python_test() {
diff --git a/sci-libs/nipype/nipype-1.8.6.ebuild b/sci-libs/nipype/nipype-1.8.6.ebuild
new file mode 100644
index 000000000..88bc23395
--- /dev/null
+++ b/sci-libs/nipype/nipype-1.8.6.ebuild
@@ -0,0 +1,97 @@
+# Copyright 1999-2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+DISTUTILS_USE_PEP517=setuptools
+PYTHON_COMPAT=( python3_{10..11} )
+PYTHON_REQ_USE="threads(+),sqlite"
+
+inherit distutils-r1
+
+DESCRIPTION="Neuroimaging in Python: Pipelines and Interfaces"
+HOMEPAGE="https://nipype.readthedocs.io/"
+SRC_URI="https://github.com/nipy/nipype/archive/${PV}.tar.gz -> ${P}.tar.gz"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+IUSE="test"
+# Tests fail with numpy import error:
+# https://github.com/nipy/nipype/issues/3626
+RESTRICT="test"
+
+DEPEND="
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/prov[${PYTHON_USEDEP}]
+ sci-libs/nibabel[${PYTHON_USEDEP}]
+ test? (
+ dev-python/mock[${PYTHON_USEDEP}]
+ dev-python/pytest[${PYTHON_USEDEP}]
+ ${RDEPEND}
+ )
+"
+
+RDEPEND="
+ dev-python/click[${PYTHON_USEDEP}]
+ dev-python/filelock[${PYTHON_USEDEP}]
+ dev-python/looseversion[${PYTHON_USEDEP}]
+ dev-python/networkx[${PYTHON_USEDEP}]
+ dev-python/packaging[${PYTHON_USEDEP}]
+ dev-python/pydot[${PYTHON_USEDEP}]
+ dev-python/python-dateutil[${PYTHON_USEDEP}]
+ dev-python/rdflib[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ dev-python/simplejson[${PYTHON_USEDEP}]
+ <dev-python/traits-6.4.0[${PYTHON_USEDEP}]
+"
+
+PATCHES=(
+ "${FILESDIR}/${PN}-1.8.4-no_etelemetry.patch"
+)
+
+src_prepare() {
+ # Remove etelemetry
+ # Doing this separately since the file is affected by another patch.
+ sed -i '/"etelemetry/d' nipype/info.py requirements.txt || die
+
+ # Mark failing tests
+ sed -i \
+ -e "/def test_no_et(tmp_path):/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-606003186')" \
+ nipype/tests/test_nipype.py || die
+ sed -i \
+ -e "/def test_fslversion():/i@pytest.mark.skip('Known to fail by upstream: https://github.com/nipy/nipype/issues/3196#issuecomment-605997462')" \
+ nipype/interfaces/fsl/tests/test_base.py || die
+ default
+}
+
+python_install_all() {
+ distutils-r1_python_install_all
+ doenvd "${FILESDIR}/98nipype"
+}
+
+# Reported upstream:
+# https://github.com/nipy/nipype/issues/3540
+EPYTEST_DESELECT=(
+ nipype/interfaces/tests/test_io.py::test_s3datagrabber_communication
+)
+
+python_test() {
+ # Setting environment variable to disable etelemetry version check:
+ # https://github.com/nipy/nipype/issues/3196#issuecomment-605980044
+ NIPYPE_NO_ET=1 epytest
+ # Upstream test configuration fails
+ #-c nipype/pytest.ini\
+ #--doctest-modules nipype\
+ #--cov nipype\
+ #--cov-config .coveragerc\
+ #--cov-report xml:cov.xml\
+}
+
+pkg_postinst() {
+ echo
+ einfo "Please run the following commands if you"
+ einfo "intend to use nipype from an existing shell:"
+ einfo "source /etc/profile"
+ echo
+}
diff --git a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
index 976a8535b..9b9233020 100644
--- a/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
+++ b/sci-libs/spyking-circus/spyking-circus-1.1.0.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/spyking-circus/spyking-circus/archive/${PV}.tar.gz -
LICENSE="CeCILL-2"
SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64"
# Wants to run mpirun (and fails)
RESTRICT="test"
@@ -27,7 +27,7 @@ RDEPEND="
>=dev-python/mpi4py-3.0.0[${PYTHON_USEDEP}]
>=dev-python/numpy-1.17.4[${PYTHON_USEDEP}]
>=dev-python/psutil-5.6.7[${PYTHON_USEDEP}]
- >=dev-python/statsmodels-0.10.1[${PYTHON_USEDEP}]
+ dev-python/statsmodels[${PYTHON_USEDEP}]
>=dev-python/tqdm-4.40.0[${PYTHON_USEDEP}]
>=dev-python/scipy-1.3.1[${PYTHON_USEDEP}]
"
diff --git a/sci-libs/torchvision/Manifest b/sci-libs/torchvision/Manifest
index 2167de395..7cf5fa956 100644
--- a/sci-libs/torchvision/Manifest
+++ b/sci-libs/torchvision/Manifest
@@ -1 +1,2 @@
DIST torchvision-0.14.1.tar.gz 9265179 BLAKE2B 0708635b00ac7c2cf4e54799f1190f01f3240f53233695819f691313b8a369b8922520e2f3cf96184bab671877b5826b84e0936d9ca5b58004d6e2a098c6cbbf SHA512 08fb1e35da1c3f1d0446ef879d9b6a7ae839a5137c3b5b46ef8111c2ae890299e2b555d1bd3b3d61f96b8778b831d8f895487cf8a4e36e371fcd4b8acda67d1f
+DIST torchvision-0.17.1.tar.gz 13091686 BLAKE2B db25faab565412f2892ca4cf8d13c459b8045aaab83009a686a93272f0b3e3e8c0da930f1d7b0682e0adc7a600195b035ca19f71fd15a26f77b349206e3ed324 SHA512 c9ef5704a337a43c1ab3a5865b2a20d09d07a9b5eeda66c7aa1e1931772bad9acee822bb400cf627960a84ace01188cd32e95f0e709eb392bf9028d36cfc50be
diff --git a/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
new file mode 100644
index 000000000..7a3637f3a
--- /dev/null
+++ b/sci-libs/torchvision/files/torchvision-0.17.1-ffmpeg-6.patch
@@ -0,0 +1,36 @@
+From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001
+From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?=
+ <zboszor@gmail.com>
+Date: Tue, 7 Nov 2023 10:43:11 +0100
+Subject: [PATCH] Fix build with ffmpeg 6.0
+MIME-Version: 1.0
+Content-Type: text/plain; charset=UTF-8
+Content-Transfer-Encoding: 8bit
+
+Signed-off-by: Zoltán Böszörményi <zboszor@gmail.com>
+---
+ torchvision/csrc/io/decoder/stream.cpp | 11 ++---------
+ 1 file changed, 2 insertions(+), 9 deletions(-)
+
+diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp
+index 0d625ef211c..8c914050587 100644
+--- a/torchvision/csrc/io/decoder/stream.cpp
++++ b/torchvision/csrc/io/decoder/stream.cpp
+@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector<DecoderMetadata>* metadata, int num_threads) {
+ codecCtx_->thread_count = num_threads;
+ } else {
+ // otherwise set sensible defaults
+- // with the special case for the different MPEG4 codecs
+- // that don't have threading context functions
+- if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) {
+- codecCtx_->thread_type = FF_THREAD_FRAME;
+- codecCtx_->thread_count = 2;
+- } else {
+- codecCtx_->thread_count = 8;
+- codecCtx_->thread_type = FF_THREAD_SLICE;
+- }
++ codecCtx_->thread_count = 8;
++ codecCtx_->thread_type = FF_THREAD_SLICE;
+ }
+
+ int ret;
diff --git a/sci-libs/torchvision/torchvision-0.17.1.ebuild b/sci-libs/torchvision/torchvision-0.17.1.ebuild
new file mode 100644
index 000000000..e0c72684c
--- /dev/null
+++ b/sci-libs/torchvision/torchvision-0.17.1.ebuild
@@ -0,0 +1,45 @@
+# Copyright 2020-2024 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_SINGLE_IMPL=1
+DISTUTILS_USE_PEP517=setuptools
+DISTUTILS_EXT=1
+inherit distutils-r1 multiprocessing
+
+DESCRIPTION="Datasets, transforms and models to specific to computer vision"
+HOMEPAGE="https://github.com/pytorch/vision"
+SRC_URI="https://github.com/pytorch/vision/archive/v${PV}.tar.gz -> ${P}.tar.gz"
+S="${WORKDIR}/vision-${PV}"
+
+LICENSE="BSD"
+SLOT="0"
+KEYWORDS="~amd64"
+RESTRICT="test"
+
+RDEPEND="
+ $(python_gen_cond_dep '
+ dev-python/numpy[${PYTHON_USEDEP}]
+ dev-python/typing-extensions[${PYTHON_USEDEP}]
+ dev-python/pillow[${PYTHON_USEDEP}]
+ dev-python/requests[${PYTHON_USEDEP}]
+ dev-python/scipy[${PYTHON_USEDEP}]
+ ')
+ sci-libs/pytorch[${PYTHON_SINGLE_USEDEP}]
+ media-video/ffmpeg:=
+"
+DEPEND="${RDEPEND}"
+
+PATCHES=( "${FILESDIR}/${PN}-0.17.1-ffmpeg-6.patch" )
+
+src_compile()
+{
+ export MAX_JOBS="$(makeopts_jobs)" # Let ninja respect MAKEOPTS
+
+ # Ensure some ext_module sources are compiled before linking
+ export MAKEOPTS="-j1"
+
+ distutils-r1_src_compile
+}
diff --git a/sci-libs/vegas/Manifest b/sci-libs/vegas/Manifest
new file mode 100644
index 000000000..c636ac4c2
--- /dev/null
+++ b/sci-libs/vegas/Manifest
@@ -0,0 +1 @@
+DIST vegas-6.0.1.tar.gz 1535565 BLAKE2B 3cd30387e9369ce7efe62e1f5838f87c73bb93e1690c131602a8e0b77a6671e9d9cadb6b909e1f9ba548cd4a32cb09bd6d1d50bfaf536b7c3fbd269c4595ed04 SHA512 ead47a9f194846d704e229d62163233a7b063dab504e665d620f59be5c9abe2b31facf14cad612b102d4bf64d60d9f6f53c0b4bca0ba78d1e62cbd9bda77e0b1
diff --git a/sci-libs/vegas/metadata.xml b/sci-libs/vegas/metadata.xml
new file mode 100644
index 000000000..8ae183900
--- /dev/null
+++ b/sci-libs/vegas/metadata.xml
@@ -0,0 +1,19 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+ <maintainer type="project">
+ <email>sci@gentoo.org</email>
+ <name>Gentoo Science Project</name>
+ </maintainer>
+ <maintainer type="person">
+ <email>alexander@neuwirth-informatik.de</email>
+ <name>Alexander Puck Neuwirth</name>
+ </maintainer>
+ <longdescription lang="en">
+ The vegas package is for evaluating multidimensional integrals using an improved version of the adaptive Monte Carlo vegas algorithm (G. P. Lepage, J. Comput. Phys. 27(1978) 192).
+ </longdescription>
+ <upstream>
+ <remote-id type="pypi">vegas</remote-id>
+ <remote-id type="github">gplepage/vegas</remote-id>
+ </upstream>
+</pkgmetadata>
diff --git a/sci-libs/vegas/vegas-6.0.1.ebuild b/sci-libs/vegas/vegas-6.0.1.ebuild
new file mode 100644
index 000000000..7654563e4
--- /dev/null
+++ b/sci-libs/vegas/vegas-6.0.1.ebuild
@@ -0,0 +1,24 @@
+EAPI=8
+
+DISTUTILS_EXT=1
+PYTHON_COMPAT=( python3_{10..12} )
+DISTUTILS_USE_PEP517=setuptools
+inherit distutils-r1 pypi
+
+DESCRIPTION="Adaptive multidimensional Monte Carlo integration."
+HOMEPAGE="https://github.com/gplepage/vegas"
+
+LICENSE="GPL-3"
+SLOT="0"
+KEYWORDS="~amd64 ~arm64"
+
+RDEPEND="
+ >=dev-python/numpy-1.16[${PYTHON_USEDEP}]
+ >=sci-libs/gvar-13.0.2[${PYTHON_USEDEP}]
+"
+DEPEND="${RDEPEND}"
+BDEPEND="
+ >=dev-python/cython-0.17[${PYTHON_USEDEP}]
+"
+
+distutils_enable_tests unittest
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0001.patch b/sci-libs/wannier90/files/wannier90-1.1-0001.patch
deleted file mode 100644
index e68c5f4fe..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0001.patch
+++ /dev/null
@@ -1,16 +0,0 @@
-diff -urN wannier90-1.1.old/src/wannier_lib.F90 wannier90-1.1.new/src/wannier_lib.F90
---- wannier90-1.1.old/src/wannier_lib.F90 2007-12-20 10:58:37.000000000 +0100
-+++ wannier90-1.1.new/src/wannier_lib.F90 2008-04-28 17:27:19.000000000 +0200
-@@ -166,6 +166,12 @@
- exclude_bands_loc(1:num_exclude_bands) = exclude_bands(1:num_exclude_bands)
- end if
-
-+ if (postproc_setup) then
-+ call kmesh_write()
-+ write(stdout,'(1x,a25,f11.3,a)') 'Time to write kmesh ',io_time(),' (sec)'
-+ write(stdout,'(/a)') ' '//trim(seedname)//'.nnkp written.'
-+ endif
-+
-
- call kmesh_dealloc()
- call param_dealloc()
diff --git a/sci-libs/wannier90/files/wannier90-1.1-0002.patch b/sci-libs/wannier90/files/wannier90-1.1-0002.patch
deleted file mode 100644
index 391a34ca2..000000000
--- a/sci-libs/wannier90/files/wannier90-1.1-0002.patch
+++ /dev/null
@@ -1,105 +0,0 @@
-diff -urN wannier90-1.1.old/src/disentangle.F90 wannier90-1.1.new/src/disentangle.F90
---- wannier90-1.1.old/src/disentangle.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/disentangle.F90 2009-03-07 15:48:05.000000000 +0100
-@@ -1784,9 +1784,9 @@
- ! [BIG ITERATION LOOP (iter)]
-
- if (.not.dis_converged) then
-- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
-- &iterations reached >>>'
-- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
-+ write(stdout,'(/5x,a)') &
-+ '<<< Warning: Maximum number of disentanglement iterations reached >>>'
-+ write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
- endif
-
- if (icompflag.eq.1) then
-@@ -2551,8 +2551,8 @@
- ! [BIG ITERATION LOOP (iter)]
-
- if (.not.dis_converged) then
-- write(stdout,'(/5x,a)') '<<< Warning: Maximum number of disentanglement &
-- &iterations reached >>>'
-+ write(stdout,'(/5x,a)') &
-+ '<<< Warning: Maximum number of disentanglement iterations reached >>>'
- write(stdout,'(10x,a)') '<<< Disentanglement convergence criteria not satisfied >>>'
- endif
-
-diff -urN wannier90-1.1.old/src/overlap.F90 wannier90-1.1.new/src/overlap.F90
---- wannier90-1.1.old/src/overlap.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/overlap.F90 2009-03-07 15:48:36.000000000 +0100
-@@ -141,8 +141,8 @@
- nn_found=.true.
- nn=inn
- else
-- call io_error('Error reading '//trim(seedname)//'.mmn.&
-- & More than one matching nearest neighbour found')
-+ call io_error('Error reading '//trim(seedname)// &
-+ '.mmn. More than one matching nearest neighbour found')
- endif
- endif
- end do
-diff -urN wannier90-1.1.old/src/parameters.F90 wannier90-1.1.new/src/parameters.F90
---- wannier90-1.1.old/src/parameters.F90 2009-03-07 15:44:11.000000000 +0100
-+++ wannier90-1.1.new/src/parameters.F90 2009-03-07 15:50:46.000000000 +0100
-@@ -1054,8 +1054,9 @@
- write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
- do nsp=1,num_species
- do nat=1,atoms_species_num(nsp)
-- write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
-- '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
-+ write(stdout,'(1x,a1,1x,a2,1x,i3,3F10.5,3x,a1,1x,3F10.5,4x,a1)') &
-+& '|',atoms_symbol(nsp),nat,atoms_pos_frac(:,nat,nsp),&
-+& '|',atoms_pos_cart(:,nat,nsp)*lenconfac,'|'
- end do
- end do
- write(stdout,'(1x,a)') '*----------------------------------------------------------------------------*'
-@@ -1073,8 +1074,8 @@
- write(stdout,'(1x,a)') '| Frac. Coord. l mr r z-axis x-axis Z/a |'
- write(stdout,'(1x,a)') '+----------------------------------------------------------------------------+'
- do nsp=1,num_proj
-- write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),&
-- & 2x,f4.1,1x,a1)') '|',proj_site(1,nsp),proj_site(2,nsp),&
-+ write(stdout,'(1x,a1,3(1x,f5.2),1x,i2,1x,i2,1x,i2,3(1x,f6.3),3(1x,f6.3),2x,f4.1,1x,a1)')&
-+& '|',proj_site(1,nsp),proj_site(2,nsp),&
- proj_site(3,nsp),proj_l(nsp), proj_m(nsp),proj_radial(nsp),&
- proj_z(1,nsp),proj_z(2,nsp),proj_z(3,nsp),proj_x(1,nsp),&
- proj_x(2,nsp),proj_x(3,nsp),proj_zona(nsp),'|'
-@@ -2738,8 +2739,8 @@
- dummy=utility_strip(in_data(line))
- dummy=adjustl(dummy)
- pos1=index(dummy,':')
-- if(pos1==0) call io_error('param_read_projection: malformed projection &
-- &definition: '//trim(dummy))
-+ if(pos1==0) &
-+ call io_error('param_read_projection: malformed projection definition: '//trim(dummy))
- sites=0
- ctemp=dummy(:pos1-1)
- ! Read the atomic site
-@@ -2980,11 +2981,11 @@
- endif
- end if
- if(sites==-1) then
-- if(counter+sum(ang_states) > num_proj) call io_error('param_get_projection: &
-- &too many projections defined')
-+ if(counter+sum(ang_states) > num_proj) &
-+ call io_error('param_get_projection: too many projections defined')
- else
-- if(counter+sites*sum(ang_states) > num_proj) call io_error('param_get_projection:&
-- & too many projections defined')
-+ if(counter+sites*sum(ang_states) > num_proj) &
-+ call io_error('param_get_projection: too many projections defined')
- end if
- !
- if(sites==-1) then
-@@ -3025,8 +3026,8 @@
-
- ! check there are enough projections and add random projections if required
- if (.not. lpartrandom) then
-- if (counter.ne.num_proj) call io_error('param_get_projections:&
-- & Fewer projections defined than the number of Wannier functions requested')
-+ if (counter.ne.num_proj) call io_error(&
-+ 'param_get_projections: Fewer projections defined than the number of Wannier functions requested')
- else
- call random_seed()
- do loop=counter+1,num_proj
diff --git a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch b/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
deleted file mode 100644
index c9656ac31..000000000
--- a/sci-libs/wannier90/files/wannier90-2.0.1.1-runtest.patch
+++ /dev/null
@@ -1,12 +0,0 @@
-diff -Naurp wannier90-2.0.1.1.orig/tests/run_test.pl wannier90-2.0.1.1/tests/run_test.pl
---- wannier90-2.0.1.1.orig/tests/run_test.pl 2016-02-08 11:51:52.000000000 +0000
-+++ wannier90-2.0.1.1/tests/run_test.pl 2017-01-05 12:10:29.584850729 +0000
-@@ -2,7 +2,7 @@
- #
- use Cwd;
- my $cwd = cwd();
--$wanex="../wannier90.x" ;
-+$wanex="../src/wannier90.x" ;
- $wanex=$cwd."/".$wanex ;
- print " Running test set of inputs\n";
- @tests_found = <./test*>;